ah, the newer version has a lot more info. See if this answers your question doug

help read_annotation NAME

function [vertices, label, colortable] = ... read_annotation(filename [, verbosity])

ARGUMENTS INPUT filename string name of annotation file to read

OPTIONAL verbosity int if true (>0), disp running output + if false (==0), be quiet and do not + display any running output

OUTPUT vertices vector vector with values running from 0 to + size(vertices)-1 label vector lookup of annotation values for + corresponding vertex index. colortable struct structure of annotation data + see below

DESCRIPTION

This function essentially reads in a FreeSurfer annotation file <filename> and returns structures and vectors that together assign each index in the surface vector to one of several structure names.

COLORTABLE STRUCTURE

Consists of the following fields: o numEntries: number of entries o orig_tab: filename of original colortable file o struct_names: cell array of structure names o table: n x 5 matrix Columns 1,2,3 are RGB values for struct color Column 4 is a flag (usually 0) Column 5 is the structure ID, calculated from R + G*2^8 + B*2^16 + flag*2^24

LABEL VECTOR

Each component of the <label> vector has a structureID value. To match the structureID value with a structure name, lookup the row index of the structureID in the 5th column of the colortable.table matrix. Use this index as an offset into the struct_names field to match the structureID with a string name.

PRECONDITIONS

o <filename> must be a valid FreeSurfer annotation file.

POSTCONDITIONS

o <colortable> will be an empty struct if not embedded in a FreeSurfer annotation file.

On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:

hi doug,

I thought so. Did I miss something obvious? My version is:

% read_annotation.m % Original Author: Bruce Fischl % CVS Revision Info: % $Author: nicks $ % $Date: 2011/03/02 00:04:12 $ % $Revision: 1.7 $

doc says:

colortable : Column 5 is the structure ID

Each component of the <label> vector has a structureID value.

Why do I get 0 in label if 0 is not in colortable.table(:, end)?

thanks Alex

On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Hi Alex, have you looked at the read_annotation help? doug

On 08/26/2013 03:37 PM, Alexandre Gramfort wrote:

...

hi,

when trying to read the following .annot file:

https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig....

using the following matlab code:

-- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) --

there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)"

the script outputs:

-- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 --

in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out?

thanks Alex _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

I think the 0s represent "unknown" areas. In this case, vertices that were not part of any cluster. Does that make sense? doug

On 08/27/2013 07:47 AM, Alexandre Gramfort wrote:

hi Doug,

I am sorry but I still don't get it.

If:

label vector lookup of annotation values for corresponding vertex index.

and label contains some 0 and 0 is not a valid id in colortable.table(:, 5) what should I do with my vertices whose label is 0?

thanks Alex

On Mon, Aug 26, 2013 at 11:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

ah, the newer version has a lot more info. See if this answers your question doug

help read_annotation NAME

     function [vertices, label, colortable] = ...
                                     read_annotation(filename [,

verbosity])

ARGUMENTS INPUT filename string name of annotation file to read

OPTIONAL verbosity int if true (>0), disp running output + if false (==0), be quiet and do not + display any running output

OUTPUT vertices vector vector with values running from 0 to + size(vertices)-1 label vector lookup of annotation values for + corresponding vertex index. colortable struct structure of annotation data + see below

DESCRIPTION

     This function essentially reads in a FreeSurfer annotation file
     <filename> and returns structures and vectors that together
     assign each index in the surface vector to one of several
     structure names.

COLORTABLE STRUCTURE

     Consists of the following fields:
     o numEntries:   number of entries
     o orig_tab:     filename of original colortable file
     o struct_names: cell array of structure names
     o table:        n x 5 matrix
                     Columns 1,2,3 are RGB values for struct color
                     Column 4 is a flag (usually 0)
                     Column 5 is the structure ID, calculated from
                     R + G*2^8 + B*2^16 + flag*2^24

LABEL VECTOR

     Each component of the <label> vector has a structureID value. To
     match the structureID value with a structure name, lookup the row
     index of the structureID in the 5th column of the colortable.table
     matrix. Use this index as an offset into the struct_names field
     to match the structureID with a string name.

PRECONDITIONS

     o <filename> must be a valid FreeSurfer annotation file.

POSTCONDITIONS

     o <colortable> will be an empty struct if not embedded in a
       FreeSurfer annotation file.

On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:

...

hi doug,

I thought so. Did I miss something obvious? My version is:

% read_annotation.m % Original Author: Bruce Fischl % CVS Revision Info: % $Author: nicks $ % $Date: 2011/03/02 00:04:12 $ % $Revision: 1.7 $

doc says:

colortable : Column 5 is the structure ID

Each component of the <label> vector has a structureID value.

Why do I get 0 in label if 0 is not in colortable.table(:, end)?

thanks Alex

On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Hi Alex, have you looked at the read_annotation help? doug

On 08/26/2013 03:37 PM, Alexandre Gramfort wrote:

...

hi,

when trying to read the following .annot file:

https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig....

using the following matlab code:

-- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) --

there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)"

the script outputs:

-- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 --

in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out?

thanks Alex _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

For aparc, that is the corpus callosum. It just means that it was in the color table when the annotation file was created. It is not necessary that it be in the annotation itself. Can you ignore it? doug

On 08/27/2013 03:33 PM, Alexandre Gramfort wrote:

hi doug,

this helps thanks. A next question is why can we have in the colortable a structureID that has no corresponding vertex with this label?

In my example it was 3834223 but I get the same thing with "fsaverage/label/lh.aparc.annot" that has a 3294840 structureID not present in the label array.

thanks Alex

On Tue, Aug 27, 2013 at 6:32 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

I think the 0s represent "unknown" areas. In this case, vertices that were not part of any cluster. Does that make sense? doug

On 08/27/2013 07:47 AM, Alexandre Gramfort wrote:

...

hi Doug,

I am sorry but I still don't get it.

If:

label vector lookup of annotation values for corresponding vertex index.

and label contains some 0 and 0 is not a valid id in colortable.table(:, 5) what should I do with my vertices whose label is 0?

thanks Alex

On Mon, Aug 26, 2013 at 11:52 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

ah, the newer version has a lot more info. See if this answers your question doug

help read_annotation NAME

      function [vertices, label, colortable] = ...
                                      read_annotation(filename [,

verbosity])

ARGUMENTS
INPUT
      filename        string          name of annotation file to read

OPTIONAL
      verbosity       int             if true (>0), disp running

output + if false (==0), be quiet and do not + display any running output

OUTPUT
      vertices        vector          vector with values running from

0 to + size(vertices)-1 label vector lookup of annotation values for + corresponding vertex index. colortable struct structure of annotation data + see below

DESCRIPTION

      This function essentially reads in a FreeSurfer annotation file
      <filename> and returns structures and vectors that together
      assign each index in the surface vector to one of several
      structure names.

COLORTABLE STRUCTURE

      Consists of the following fields:
      o numEntries:   number of entries
      o orig_tab:     filename of original colortable file
      o struct_names: cell array of structure names
      o table:        n x 5 matrix
                      Columns 1,2,3 are RGB values for struct color
                      Column 4 is a flag (usually 0)
                      Column 5 is the structure ID, calculated from
                      R + G*2^8 + B*2^16 + flag*2^24

LABEL VECTOR

      Each component of the <label> vector has a structureID value. To
      match the structureID value with a structure name, lookup the

row index of the structureID in the 5th column of the colortable.table matrix. Use this index as an offset into the struct_names field to match the structureID with a string name.

PRECONDITIONS

      o <filename> must be a valid FreeSurfer annotation file.

POSTCONDITIONS

      o <colortable> will be an empty struct if not embedded in a
        FreeSurfer annotation file.

On 08/26/2013 05:35 PM, Alexandre Gramfort wrote:

...

hi doug,

I thought so. Did I miss something obvious? My version is:

% read_annotation.m % Original Author: Bruce Fischl % CVS Revision Info: % $Author: nicks $ % $Date: 2011/03/02 00:04:12 $ % $Revision: 1.7 $

doc says:

colortable : Column 5 is the structure ID

Each component of the <label> vector has a structureID value.

Why do I get 0 in label if 0 is not in colortable.table(:, end)?

thanks Alex

On Mon, Aug 26, 2013 at 10:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

Hi Alex, have you looked at the read_annotation help? doug

On 08/26/2013 03:37 PM, Alexandre Gramfort wrote: > hi, > > when trying to read the following .annot file: > > > > https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig.... > > using the following matlab code: > > -- > [vertices, label, colortable] = > read_annotation('left_mc-z.negative.sig.ocn.annot'); > unique(label) > unique(colortable.table(:, end)) > setdiff(colortable.table(:, end), unique(label)) > -- > > there seem to be a discrepancy between the "label" and the last column > of colortable "colortable.table(:, end)" > > the script outputs: > > -- > Reading from version 2 > colortable with 7 entries read (originally none) > ans = > 0 2244856 3987639 5840816 11298645 > 13698134 16665710 > ans = > 2244856 3834223 3987639 5840816 11298645 > 13698134 16665710 > ans = > 3834223 > -- > > in other words 0 is in label but not in the colortable. Should I > conclude that 0 is 3834223? > If so what's the proper way of figuring this out? > > thanks > Alex > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

>

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/